Is there a way to have Cycles skip rendering alpha?
There is nothing specifically designed into Blender to tell it to ignore the transparent areas currently.

That being said, there are some things we can do to help speed up the render somewhat.


Transparent Background - Choose transparent in the Film section of the Render properties panel. This will render faster than a coloured background (whether full black or not)





Tile Size- Choose a smaller tile size than your current (this tip is mostly for CPU rendering as GPU rendering generally uses larger tiles). This will help the render times when the buckets are processing the edge of the foreground element. 





Targeted Sampling - Use the Branched Path Tracing option in the Sampling section of the Render Properties panel. If you reduce the AA sample some what and raise the bounce samples (Diffuse, Glossy, etc.), you will reduce time spent on rendering the sky/transparent background.





Cropped Render - this option is a little more extreme, but if you    have an object that doesn't move much on screen, you can crop the    render to only include the portions of the screen it's in. You'd then    composite it together with the rest of the full frame renders.